A design where the interrupt requires the reception of two characters is a design that will lock up if you get a transfer error or for some other reason only get a single character.

The idea is broken, and should be abandoned. Let your interrupt accept characters and place them in a queue. Let your main task pick up and perform actions. And let your main task decide what to do if a command byte isn't followed by a data byte within the expected time. But do not try to complicate your interrupts and at the same time lock up your processor busy-waiting for what may never arrive.